Locus 2179

Sequence ID X_DroMel_CAF1
Location 5,902,277 – 5,902,417
Length 140
Max. P 0.957408
window3534 window3535 window3536

overview

Window 4

Location 5,902,277 – 5,902,385
Length 108
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 82.66
Mean single sequence MFE -25.57
Consensus MFE -15.16
Energy contribution -16.72
Covariance contribution 1.56
Combinations/Pair 1.19
Mean z-score -2.77
Structure conservation index 0.59
SVM decision value 1.38
SVM RNA-class probability 0.948372
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5902277 108 + 22224390
GGAAAAUGCCCAACUGGAUGCUGGGCAACUGAAAAGUAUACAGAUAUAUAUAUAUAUCUGCAUAUGUGCACAUGUGCAGAGAAAGUUAUGUCCACAAAUAAUUACUAC
......((((((.(.....).))))))(((....))).....((((((........((((((((((....))))))))))......))))))................ ( -30.94)
>DroSec_CAF1 18944 99 + 1
GGAAAAUGCCCAACUGGAUGCUGGGCAACUGAAAAGUAUGCAUAUA-GUAUAUA--------UAUGUGCAUAUGUGCAGAGAAAGUCAUGUCCACAAAUAAUUACUAC
(((...((((((.(.....).)))))).(((....(((((((((((-.......--------)))))))))))...)))...........)))............... ( -29.40)
>DroSim_CAF1 16311 99 + 1
GGAAAAUGCCCAACUGGAUGCUGGGCAACUGAAAAGUAUGCAUAUA-GUAUAUA--------UAUGUGCAUAUGUGCAGAGAAAGUCAUGUCCACAAAUAAUUACUAC
(((...((((((.(.....).)))))).(((....(((((((((((-.......--------)))))))))))...)))...........)))............... ( -29.40)
>DroEre_CAF1 18955 92 + 1
GGAAAAUGCCCAACGGGAUGCUGGACAACUGAAAC-------UAUA-CCAUGU--------GCGCAUGCAUAUGUGCAGAGAAAGUCAUGUCCACAAAUAAUUACUAC
........(((...))).((.(((((((((....(-------(.((-(.((((--------((....))))))))).))....)))..))))))))............ ( -20.40)
>DroYak_CAF1 19258 95 + 1
GGAAAAUGCCCAACUGGAAGCUGGACAACUGACUA-------UAUG-GCAUAC-----UACUUAUAUGCAUAUGUGCAGAGAAAGUCAUGUCCACAAAUAAUUACUAC
.......((((....))..))((((((..((((((-------((((-(((((.-----......))))).)))))........))))))))))).............. ( -17.70)
>consensus
GGAAAAUGCCCAACUGGAUGCUGGGCAACUGAAAAGUAU_CAUAUA_GUAUAUA________UAUGUGCAUAUGUGCAGAGAAAGUCAUGUCCACAAAUAAUUACUAC
(((...((((((.(.....).)))))).(((.........((((((.(((((((........))))))).)))))))))...........)))............... (-15.16 = -16.72 +   1.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,902,277 – 5,902,385
Length 108
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 82.66
Mean single sequence MFE -24.61
Consensus MFE -18.00
Energy contribution -17.60
Covariance contribution -0.40
Combinations/Pair 1.11
Mean z-score -2.33
Structure conservation index 0.73
SVM decision value 1.39
SVM RNA-class probability 0.949490
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5902277 108 - 22224390
GUAGUAAUUAUUUGUGGACAUAACUUUCUCUGCACAUGUGCACAUAUGCAGAUAUAUAUAUAUAUCUGUAUACUUUUCAGUUGCCCAGCAUCCAGUUGGGCAUUUUCC
............((((.((((..............)))).))))((((((((((((....)))))))))))).........((((((((.....))))))))...... ( -32.34)
>DroSec_CAF1 18944 99 - 1
GUAGUAAUUAUUUGUGGACAUGACUUUCUCUGCACAUAUGCACAUA--------UAUAUAC-UAUAUGCAUACUUUUCAGUUGCCCAGCAUCCAGUUGGGCAUUUUCC
((((((..(((.((((.(.(((............))).).)))).)--------))..)))-)))................((((((((.....))))))))...... ( -23.50)
>DroSim_CAF1 16311 99 - 1
GUAGUAAUUAUUUGUGGACAUGACUUUCUCUGCACAUAUGCACAUA--------UAUAUAC-UAUAUGCAUACUUUUCAGUUGCCCAGCAUCCAGUUGGGCAUUUUCC
((((((..(((.((((.(.(((............))).).)))).)--------))..)))-)))................((((((((.....))))))))...... ( -23.50)
>DroEre_CAF1 18955 92 - 1
GUAGUAAUUAUUUGUGGACAUGACUUUCUCUGCACAUAUGCAUGCGC--------ACAUGG-UAUA-------GUUUCAGUUGUCCAGCAUCCCGUUGGGCAUUUUCC
...............(((...((((..((.(((.(((.(((....))--------).))))-)).)-------)....))))(((((((.....)))))))....))) ( -20.70)
>DroYak_CAF1 19258 95 - 1
GUAGUAAUUAUUUGUGGACAUGACUUUCUCUGCACAUAUGCAUAUAAGUA-----GUAUGC-CAUA-------UAGUCAGUUGUCCAGCUUCCAGUUGGGCAUUUUCC
............(((((.((((((((....((((....))))...)))).-----.)))))-))))-------........((((((((.....))))))))...... ( -23.00)
>consensus
GUAGUAAUUAUUUGUGGACAUGACUUUCUCUGCACAUAUGCACAUA________UAUAUAC_UAUAUG_AUACUUUUCAGUUGCCCAGCAUCCAGUUGGGCAUUUUCC
...(((..(((.((..((.(......).))..)).))))))........................................((((((((.....))))))))...... (-18.00 = -17.60 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,902,305 – 5,902,417
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 80.76
Mean single sequence MFE -26.95
Consensus MFE -18.12
Energy contribution -17.20
Covariance contribution -0.92
Combinations/Pair 1.25
Mean z-score -2.35
Structure conservation index 0.67
SVM decision value 1.48
SVM RNA-class probability 0.957408
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5902305 112 - 22224390
UUU--------UCGGUUGCGUCUUCUUAGGCAGCCGAAAUGUAGUAAUUAUUUGUGGACAUAACUUUCUCUGCACAUGUGCACAUAUGCAGAUAUAUAUAUAUAUCUGUAUACUUUUCAG
.((--------((((((((.(......).)))))))))).............((((.((((..............)))).))))((((((((((((....))))))))))))........ ( -33.24)
>DroSec_CAF1 18972 103 - 1
UUU--------UCGGUUGCGUCUUCUUAGGCAGCCGAAAUGUAGUAAUUAUUUGUGGACAUGACUUUCUCUGCACAUAUGCACAUA--------UAUAUAC-UAUAUGCAUACUUUUCAG
..(--------((((((((.(......).)))))))))((((((((..(((.((((.(.(((............))).).)))).)--------))..)))-)))))............. ( -26.10)
>DroSim_CAF1 16339 103 - 1
UUU--------UCGGUUGCGUCUUCUUAGGCAGCCGAAAUGUAGUAAUUAUUUGUGGACAUGACUUUCUCUGCACAUAUGCACAUA--------UAUAUAC-UAUAUGCAUACUUUUCAG
..(--------((((((((.(......).)))))))))((((((((..(((.((((.(.(((............))).).)))).)--------))..)))-)))))............. ( -26.10)
>DroEre_CAF1 18983 97 - 1
UUUU-------UUGGUUGCGUCUUCUUGGGCAGCUGAAAUGUAGUAAUUAUUUGUGGACAUGACUUUCUCUGCACAUAUGCAUGCGC--------ACAUGG-UAUA-------GUUUCAG
..((-------(..(((((.((.....)))))))..)))....(.((((((.((..((.(......).))..))(((.(((....))--------).))).-.)))-------))).).. ( -19.50)
>DroYak_CAF1 19286 107 - 1
UUUUCUGUGUUUCGGUUGCGUCUUCUUAGGCAGCUGAAAUGUAGUAAUUAUUUGUGGACAUGACUUUCUCUGCACAUAUGCAUAUAAGUA-----GUAUGC-CAUA-------UAGUCAG
....(((..((((((((((.(......).))))))))))..)))........(((((.((((((((....((((....))))...)))).-----.)))))-))))-------....... ( -29.80)
>consensus
UUU________UCGGUUGCGUCUUCUUAGGCAGCCGAAAUGUAGUAAUUAUUUGUGGACAUGACUUUCUCUGCACAUAUGCACAUA________UAUAUAC_UAUAUG_AUACUUUUCAG
...........((((((((.(......).)))))))).((((.(((..(((.((..((.(......).))..)).))))))))))................................... (-18.12 = -17.20 +  -0.92)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:05 2006